CANEapp

CANEapp automates analysis of RNA-seq data from next-generation sequencing (NGS) experiments to perform differential gene expression and novel noncoding RNA discovery.

Key Features:

• Automated server-side pipeline: Provides an automated server-side pipeline for processing RNA-seq datasets.
• Automated installation on Linux: Performs automated installation of software components and reference files on a Linux server.
• Platform independence and scalability: Adapts to different server architectures and efficiently utilizes computational resources to manage large datasets.
• Comprehensive analysis workflows: Supports differential gene expression and novel noncoding RNA discovery using workflows including Cuffdiff and the R packages edgeR and DESeq2.
• Experimental validation: Performance has been validated on biological datasets with confirmation by quantitative real-time PCR (qRT-PCR).

Scientific Applications:

• Differential gene expression analysis: Detects and quantifies differential expression from RNA-seq NGS datasets.
• Novel noncoding RNA discovery: Identifies candidate novel noncoding RNAs from RNA-seq data using alternative analysis workflows.
• High-throughput RNA-seq processing: Processes and scales analyses for large RNA-seq experiments across diverse server environments.

Methodology:

Automated server-side pipeline installs required software and reference files on a Linux server and executes analysis workflows using Cuffdiff and the R packages edgeR and DESeq2.